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Wongsirichot P, Barroso-Ingham B, Hamilton A, Parroquin Gonzalez M, Romero Jimenez R, Hoeven R, Winterburn J. Food wastes for bioproduct production and potential strategies for high feedstock variability. WASTE MANAGEMENT (NEW YORK, N.Y.) 2024; 184:1-9. [PMID: 38781721 DOI: 10.1016/j.wasman.2024.05.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 04/12/2024] [Accepted: 05/20/2024] [Indexed: 05/25/2024]
Abstract
Unavoidable food wastes could be an important feedstock for industrial biotechnology, while their valorization could provide added value for the food processor. However, despite their abundance and low costs, the heterogeneous/mixed nature of these food wastes produced by food processors and consumers leads to a high degree of variability in carbon and nitrogen content, as well as specific substrates, in food waste hydrolysate. This has limited their use for bioproduct synthesis. These wastes are often instead used in anaerobic digestion and mixed microbial culture, creating a significant knowledge gap in their use for higher value biochemical production via pure and single microbial culture. To directly investigate this knowledge gap, various waste streams produced by a single food processor were enzymatically hydrolyzed and characterized, and the degree of variability with regard to substrates, carbon, and nitrogen was quantified. The impact of hydrolysate variability on the viability and performance of polyhydroxyalkanoates biopolymers production using bacteria (Cupriavidus necator) and archaea (Haloferax mediterranei) as well as sophorolipids biosurfactants production with the yeast (Starmerella bombicola) was then elucidated at laboratory-scale. After which, strategies implemented during this experimental proof-of-concept study, and beyond, for improved industrial-scale valorization which addresses the high variability of food waste hydrolysate were discussed in-depth, including media standardization and high non-selective microbial organisms growth-associated product synthesis. The insights provided would be beneficial for future endeavors aiming to utilize food wastes as feedstocks for industrial biotechnology.
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Affiliation(s)
- Phavit Wongsirichot
- Department of Chemical Engineering, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Benjamin Barroso-Ingham
- Department of Chemical Engineering, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Alexander Hamilton
- Department of Chemical Engineering, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Mariana Parroquin Gonzalez
- Department of Chemical Engineering, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Roger Romero Jimenez
- Department of Chemical Engineering, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Robin Hoeven
- Department of Chemical Engineering, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - James Winterburn
- Department of Chemical Engineering, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
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Chu PH, Jenol MA, Phang LY, Ibrahim MF, Purkan P, Hadi S, Abd-Aziz S. Innovative approaches for amino acid production via consolidated bioprocessing of agricultural biomass. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:33303-33324. [PMID: 38710845 DOI: 10.1007/s11356-024-33534-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Accepted: 04/27/2024] [Indexed: 05/08/2024]
Abstract
Agricultural plantations in Indonesia and Malaysia yield substantial waste, necessitating proper disposal to address environmental concerns. Yet, these wastes, rich in starch and lignocellulosic content, offer an opportunity for value-added product development, particularly amino acid production. Traditional methods often rely on costly commercial enzymes to convert biomass into fermentable sugars for amino acid production. An alternative, consolidated bioprocessing, enables the direct conversion of agricultural biomass into amino acids using selected microorganisms. This review provides a comprehensive assessment of the potential of agricultural biomass in Indonesia and Malaysia for amino acid production through consolidated bioprocessing. It explores suitable microorganisms and presents a case study on using Bacillus subtilis ATCC 6051 to produce 9.56 mg/mL of amino acids directly from pineapple plant stems. These findings contribute to the advancement of sustainable amino acid production methods using agricultural biomass especially in Indonesia and Malaysia through consolidated bioprocessing, reducing waste and enhancing environmental sustainability.
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Affiliation(s)
- Pei-Hsia Chu
- Department of Bioprocess Technology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Mohd Azwan Jenol
- Department of Bioprocess Technology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Lai-Yee Phang
- Department of Bioprocess Technology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Mohamad Faizal Ibrahim
- Department of Bioprocess Technology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Purkan Purkan
- Biochemistry Division, Department of Chemistry, Faculty of Science and Technology, Airlangga University, Jl. Mulyorejo, Surabaya, 60115, Indonesia
| | - Sofijan Hadi
- Biochemistry Division, Department of Chemistry, Faculty of Science and Technology, Airlangga University, Jl. Mulyorejo, Surabaya, 60115, Indonesia
| | - Suraini Abd-Aziz
- Department of Bioprocess Technology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
- Biochemistry Division, Department of Chemistry, Faculty of Science and Technology, Airlangga University, Jl. Mulyorejo, Surabaya, 60115, Indonesia.
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Das Baksi K, Pokhrel V, Pudavar AE, Mande SS, Kuntal BK. BactInt: A domain driven transfer learning approach for extracting inter-bacterial associations from biomedical text. Comput Biol Chem 2024; 109:108012. [PMID: 38198963 DOI: 10.1016/j.compbiolchem.2023.108012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 12/15/2023] [Accepted: 12/30/2023] [Indexed: 01/12/2024]
Abstract
BACKGROUND The healthy as well as dysbiotic state of an ecosystem like human body is known to be influenced not only by the presence of the bacterial groups in it, but also with respect to the associations within themselves. Evidence reported in biomedical text serves as a reliable source for identifying and ascertaining such inter bacterial associations. However, the complexity of the reported text as well as the ever-increasing volume of information necessitates development of methods for automated and accurate extraction of such knowledge. METHODS A BioBERT (biomedical domain specific language model) based information extraction model for bacterial associations is presented that utilizes learning patterns from other publicly available datasets. Additionally, a specialized sentence corpus has been developed to significantly improve the prediction accuracy of the 'transfer learned' model using a fine-tuning approach. RESULTS The final model was seen to outperform all other variations (non-transfer learned and non-fine-tuned models) as well as models trained on BioGPT (a domain trained Generative Pre-trained Transformer). To further demonstrate the utility, a case study was performed using bacterial association network data obtained from experimental studies. CONCLUSION This study attempts to demonstrate the applicability of transfer learning in a niche field of life sciences where understanding of inter bacterial relationships is crucial to obtain meaningful insights in comprehending microbial community structures across different ecosystems. The study further discusses how such a model can be further improved by fine tuning using limited training data. The results presented and the datasets made available are expected to be a valuable addition in the field of medical informatics and bioinformatics.
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Affiliation(s)
| | - Vatsala Pokhrel
- TCS Research, Tata Consultancy Services Ltd, Pune 411057, India
| | | | | | - Bhusan K Kuntal
- TCS Research, Tata Consultancy Services Ltd, Pune 411057, India.
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Hernández-Guerrero M, Gomez-Maldonado D, Gutiérrez-Castañeda J, Revah S, Campos-Terán J, Vigueras-Ramírez G. Assessment of Culture Systems to Produce Bacterial Cellulose with a Kombucha Consortium. Appl Biochem Biotechnol 2024:10.1007/s12010-024-04929-z. [PMID: 38558275 DOI: 10.1007/s12010-024-04929-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/18/2024] [Indexed: 04/04/2024]
Abstract
Bacterial cellulose (BC) is an emerging material for high-end applications due to its biocompatibility and physicochemical characteristics. However, the scale-up production of this material is still expensive, with the culture medium constituting one-third of the total cost. Herein, four different media (yeast nitrogen base, YNB; Murashige and Skoog, MSO; black tea; and NPK fertilizer solution) were compared while using sucrose as an additional carbon source. The yields of BC were best for YNB and fertilizer with 0.37 and 0.34 gBC/gC respectively. These two were then compared using glucose as a carbon source, with improvements in the production of 29% for the fertilizer, while only an 8% increase for YNB was seen; however, as the carbon concentration increased with a fixed N concentration, the yield was lower but the rate of production of BC increased. The obtained BC films were sanitized and showed low molecular weight and all the expected cellulose characteristic FT-IR bands while SEM showed nanofibers around 0.1 μm. Compared to traditional methods for lab-scale production, the use of the fertilizer and the consortium represent benefits compared to traditional lab-scale BC culture methods such as a competitive cost (two times lower) while posing resilience and tolerance to stress conditions given that it is produced by microbial communities and not with a single strain. Additionally, the low molecular weight of the films could be of interest for certain coating formulations.
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Affiliation(s)
- Maribel Hernández-Guerrero
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana-Cuajimalpa, Vasco de Quiroga 4871, Cuajimalpa, 05348, Mexico City, Mexico
| | - Diego Gomez-Maldonado
- Department of Chemical Engineering, Northeastern University, 360 Huntington Ave, Boston, MA, 02115, USA
| | - Jorge Gutiérrez-Castañeda
- Ingeniería Biológica, Universidad Autónoma Metropolitana-Cuajimalpa, Vasco de Quiroga 4871, Cuajimalpa, 05348, Mexico City, Mexico
| | - Sergio Revah
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana-Cuajimalpa, Vasco de Quiroga 4871, Cuajimalpa, 05348, Mexico City, Mexico
| | - José Campos-Terán
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana-Cuajimalpa, Vasco de Quiroga 4871, Cuajimalpa, 05348, Mexico City, Mexico
| | - Gabriel Vigueras-Ramírez
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana-Cuajimalpa, Vasco de Quiroga 4871, Cuajimalpa, 05348, Mexico City, Mexico.
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Wang N, Wang X, Chen L, Liu H, Wu Y, Huang M, Fang L. Biological roles of soil microbial consortium on promoting safe crop production in heavy metal(loid) contaminated soil: A systematic review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:168994. [PMID: 38043809 DOI: 10.1016/j.scitotenv.2023.168994] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 11/08/2023] [Accepted: 11/27/2023] [Indexed: 12/05/2023]
Abstract
Heavy metal(loid) (HM) pollution of agricultural soils is a growing global environmental concern that affects planetary health. Numerous studies have shown that soil microbial consortia can inhibit the accumulation of HMs in crops. However, our current understanding of the effects and mechanisms of inhibition is fragmented. In this review, we summarise extant studies and knowledge to provide a comprehensive view of HM toxicity on crop growth and development at the biological, cellular and the molecular levels. In a meta-analysis, we find that microbial consortia can improve crop resistance and reduce HM uptake, which in turn promotes healthy crop growth, demonstrating that microbial consortia are more effective than single microorganisms. We then review three main mechanisms by which microbial consortia reduce the toxicity of HMs to crops and inhibit HMs accumulation in crops: 1) reducing the bioavailability of HMs in soil (e.g. biosorption, bioaccumulation and biotransformation); 2) improving crop resistance to HMs (e.g. facilitating the absorption of nutrients); and 3) synergistic effects between microorganisms. Finally, we discuss the prospects of microbial consortium applications in simultaneous crop safety production and soil remediation, indicating that they play a key role in sustainable agricultural development, and conclude by identifying research challenges and future directions for the microbial consortium to promote safe crop production.
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Affiliation(s)
- Na Wang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, The Research Center of Soil and Water Conservation and Ecological Environment, CAS and MOE, Yangling 712100, China; State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, CAS and MWR, Yangling 712100, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiangxiang Wang
- College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, China
| | - Li Chen
- College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, China
| | - Hongjie Liu
- College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, China
| | - Yanfang Wu
- Palm Eco-Town Development Co., Ltd., Zhengzhou 450000, China
| | - Min Huang
- Key Laboratory of Green Utilization of Critical Nonmetallic Mineral Resources, Ministry of Education, Wuhan University of Technology, Wuhan 430070, China
| | - Linchuan Fang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, The Research Center of Soil and Water Conservation and Ecological Environment, CAS and MOE, Yangling 712100, China; State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, CAS and MWR, Yangling 712100, China; Key Laboratory of Green Utilization of Critical Nonmetallic Mineral Resources, Ministry of Education, Wuhan University of Technology, Wuhan 430070, China.
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Benninghaus L, Schwardmann LS, Jilg T, Wendisch VF. Establishment of synthetic microbial consortia with Corynebacterium glutamicum and Pseudomonas putida: Design, construction, and application to production of γ-glutamylisopropylamide and l-theanine. Microb Biotechnol 2024; 17:e14400. [PMID: 38206115 PMCID: PMC10832564 DOI: 10.1111/1751-7915.14400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 12/18/2023] [Accepted: 12/21/2023] [Indexed: 01/12/2024] Open
Abstract
Microbial synthetic consortia are a promising alternative to classical monoculture for biotechnological applications and fermentative processes. Their versatile use offers advantages in the degradation of complex substrates, the allocation of the metabolic burden between individual partners, or the division of labour in energy utilisation, substrate supply or product formation. Here, stable synthetic consortia between the two industrially relevant production hosts, Pseudomonas putida KT2440 and Corynebacterium glutamicum ATCC13032, were established for the first time. By applying arginine auxotrophy/overproduction and/or formamidase-based utilisation of the rare nitrogen source formamide, different types of interaction were realised, such as commensal relationships (+/0 and 0/+) and mutualistic cross-feeding (+/+). These consortia did not only show stable growth but could also be used for fermentative production of the γ-glutamylated amines theanine and γ-glutamyl-isopropylamide (GIPA). The consortia produced up to 2.8 g L-1 of GIPA and up to 2.6 g L-1 of theanine, a taste-enhancing constituent of green tea leaves. Thus, the advantageous approach of using synthetic microbial consortia for fermentative production of value-added compounds was successfully demonstrated.
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Affiliation(s)
- Leonie Benninghaus
- Genetics of Prokaryotes, Faculty of Biology and CeBiTecBielefeld UniversityBielefeldGermany
| | - Lynn S. Schwardmann
- Genetics of Prokaryotes, Faculty of Biology and CeBiTecBielefeld UniversityBielefeldGermany
- Present address:
Aminoverse B.V.Daelderweg 9Nuth6361 HKthe Netherlands
| | - Tatjana Jilg
- Genetics of Prokaryotes, Faculty of Biology and CeBiTecBielefeld UniversityBielefeldGermany
- Present address:
Symrise AGMühlenfeldstraße 1Holzminden37603Germany
| | - Volker F. Wendisch
- Genetics of Prokaryotes, Faculty of Biology and CeBiTecBielefeld UniversityBielefeldGermany
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Bounaga A, Alsanea A, Danouche M, Rittmann BE, Zhou C, Boulif R, Zeroual Y, Benhida R, Lyamlouli K. Effect of alkaline leaching of phosphogypsum on sulfate reduction activity and bacterial community composition using different sources of anaerobic microbial inoculum. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 904:166296. [PMID: 37591387 DOI: 10.1016/j.scitotenv.2023.166296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/17/2023] [Accepted: 08/12/2023] [Indexed: 08/19/2023]
Abstract
Phosphogypsum (PG), a by-product of the phosphate industry, is high in sulfate, (SO42-), which makes it an excellent substrate for sulfate-reducing bacteria (SRB) to produce hydrogen sulfide. This work aimed to optimize SO42- leaching from PG to achieve a high biological reduction of SO42- and generate high sulfide concentrations for subsequent use in the biological recovery of elemental sulfur. Five SRB consortia were isolated and enriched from: IS (Industrial sludges), MS (Marine sediments), WC (Winogradsky column), SNV (petroleum industry sediments) and PG (stored Phosphogypsum). The five consortia showed reduction activity when using PG leachate (with water) as source of SO42- and lactate, acetate, or glucose as the electron donor. The highest reduction rate (81.5 %) was registered using lactate and the IS consortium (81.5 %) followed by MS (79 %) and PG (71 %). To enhance the concentration of leached SO42- from PG for future utilization with the isolated consortia, PG was treated with NaOH solutions (2 % and 5 %). SO42- release of 97 % was achieved with a 5 % concentration and the resulting leachate was further diluted to target a SO42- concentration of 12.4 g·L-1 for utilization with the isolated consortia. Compared to water leachate, a significantly higher reduction rate was registered (2 g·L-1 of SO42) using the IS consortium, demonstrating limited inhibition effect of sulfide- concentration on SRB functionalities. Moreover, metagenomic analysis of the consortia revealed that using PG as a source of SO42- increased the abundance of Deltaproteobacteria, including known SRB like Desulfovibrio, Desulfomicrobium, and Desulfosporosinus, as well as novel SRB genera (Cupidesulfovibrio, Desulfocurvus, Desulfococcus) that showed, for the first time, significant potential as novel sulfate-reducers using PG as a SO42- source.
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Affiliation(s)
- Ayoub Bounaga
- Department of Chemical & Biochemical Sciences-Green Process Engineering (CBS), Mohammed VI Polytechnic University (UM6P), Benguerir, 43150, Morocco
| | - Anwar Alsanea
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, P.O. Box 875017, Tempe, AZ 85287-5701, USA
| | - Mohammed Danouche
- Department of Chemical & Biochemical Sciences-Green Process Engineering (CBS), Mohammed VI Polytechnic University (UM6P), Benguerir, 43150, Morocco
| | - Bruce E Rittmann
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, P.O. Box 875017, Tempe, AZ 85287-5701, USA
| | - Chen Zhou
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, P.O. Box 875017, Tempe, AZ 85287-5701, USA
| | - Rachid Boulif
- Department of Chemical & Biochemical Sciences-Green Process Engineering (CBS), Mohammed VI Polytechnic University (UM6P), Benguerir, 43150, Morocco
| | - Youssef Zeroual
- Situation Innovation, OCP Group BP 118, Jorf Lasfar El Jadida 24000, Morocco
| | - Rachid Benhida
- Department of Chemical & Biochemical Sciences-Green Process Engineering (CBS), Mohammed VI Polytechnic University (UM6P), Benguerir, 43150, Morocco; Institute of Chemistry, Nice UMR7272, Côte d'Azur University, French National Centre for Scientific Research (CNRS), Nice, France
| | - Karim Lyamlouli
- College of Sustainable Agriculture and Environmental Sciences, Agrobioscience program, Mohammed VI Polytechnic University, Benguerir 43150, Morocco.
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8
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Gong P, Tang J, Wang J, Wang C, Chen W. A Novel Microbial Consortia Catalysis Strategy for the Production of Hydroxytyrosol from Tyrosine. Int J Mol Sci 2023; 24:ijms24086944. [PMID: 37108108 PMCID: PMC10139182 DOI: 10.3390/ijms24086944] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 04/04/2023] [Accepted: 04/06/2023] [Indexed: 04/29/2023] Open
Abstract
Hydroxytyrosol, a valuable plant-derived phenolic compound, is increasingly produced from microbial fermentation. However, the promiscuity of the key enzyme HpaBC, the two-component flavin-dependent monooxygenase from Escherichia coli, often leads to low yields. To address this limitation, we developed a novel strategy utilizing microbial consortia catalysis for hydroxytyrosol production. We designed a biosynthetic pathway using tyrosine as the substrate and selected enzymes and overexpressing glutamate dehydrogenase GdhA to realize the cofactor cycling by coupling reactions catalyzed by the transaminase and the reductase. Additionally, the biosynthetic pathway was divided into two parts and performed by separate E. coli strains. Furthermore, we optimized the inoculation time, strain ratio, and pH to maximize the hydroxytyrosol yield. Glycerol and ascorbic acid were added to the co-culture, resulting in a 92% increase in hydroxytyrosol yield. Using this approach, the production of 9.2 mM hydroxytyrosol was achieved from 10 mM tyrosine. This study presents a practical approach for the microbial production of hydroxytyrosol that can be promoted to produce other value-added compounds.
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Affiliation(s)
- Pengfei Gong
- Key Laboratory of Geriatric Nutrition and Health, Ministry of Education, Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center of Food Additives, School of Food and Health, Beijing Technology and Business University, Beijing 100048, China
| | - Jiali Tang
- Key Laboratory of Geriatric Nutrition and Health, Ministry of Education, Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center of Food Additives, School of Food and Health, Beijing Technology and Business University, Beijing 100048, China
| | - Jiaying Wang
- Key Laboratory of Geriatric Nutrition and Health, Ministry of Education, Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center of Food Additives, School of Food and Health, Beijing Technology and Business University, Beijing 100048, China
| | - Chengtao Wang
- Key Laboratory of Geriatric Nutrition and Health, Ministry of Education, Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center of Food Additives, School of Food and Health, Beijing Technology and Business University, Beijing 100048, China
| | - Wei Chen
- Key Laboratory of Geriatric Nutrition and Health, Ministry of Education, Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center of Food Additives, School of Food and Health, Beijing Technology and Business University, Beijing 100048, China
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Hengsbach JN, Sabel-Becker B, Ulber R, Holtmann D. Microbial electrosynthesis of methane and acetate—comparison of pure and mixed cultures. Appl Microbiol Biotechnol 2022; 106:4427-4443. [PMID: 35763070 PMCID: PMC9259517 DOI: 10.1007/s00253-022-12031-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 06/13/2022] [Accepted: 06/14/2022] [Indexed: 12/01/2022]
Abstract
Abstract The electrochemical process of microbial electrosynthesis (MES) is used to drive the metabolism of electroactive microorganisms for the production of valuable chemicals and fuels. MES combines the advantages of electrochemistry, engineering, and microbiology and offers alternative production processes based on renewable raw materials and regenerative energies. In addition to the reactor concept and electrode design, the biocatalysts used have a significant influence on the performance of MES. Thus, pure and mixed cultures can be used as biocatalysts. By using mixed cultures, interactions between organisms, such as the direct interspecies electron transfer (DIET) or syntrophic interactions, influence the performance in terms of productivity and the product range of MES. This review focuses on the comparison of pure and mixed cultures in microbial electrosynthesis. The performance indicators, such as productivities and coulombic efficiencies (CEs), for both procedural methods are discussed. Typical products in MES are methane and acetate, therefore these processes are the focus of this review. In general, most studies used mixed cultures as biocatalyst, as more advanced performance of mixed cultures has been seen for both products. When comparing pure and mixed cultures in equivalent experimental setups a 3-fold higher methane and a nearly 2-fold higher acetate production rate can be achieved in mixed cultures. However, studies of pure culture MES for methane production have shown some improvement through reactor optimization and operational mode reaching similar performance indicators as mixed culture MES. Overall, the review gives an overview of the advantages and disadvantages of using pure or mixed cultures in MES. Key points • Undefined mixed cultures dominate as inoculums for the MES of methane and acetate, which comprise a high potential of improvement • Under similar conditions, mixed cultures outperform pure cultures in MES • Understanding the role of single species in mixed culture MES is essential for future industrial applications
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Affiliation(s)
- Jan-Niklas Hengsbach
- Department of Mechanical and Process Engineering, Institute of Bioprocess Engineering, Technical University Kaiserslautern, 67663, Kaiserslautern, Germany
| | - Björn Sabel-Becker
- Department of Life Science Engineering, Institute of Bioprocess Engineering and Pharmaceutical Technology, Technische Hochschule Mittelhessen, 35390, Giessen, Germany
| | - Roland Ulber
- Department of Mechanical and Process Engineering, Institute of Bioprocess Engineering, Technical University Kaiserslautern, 67663, Kaiserslautern, Germany.
| | - Dirk Holtmann
- Department of Life Science Engineering, Institute of Bioprocess Engineering and Pharmaceutical Technology, Technische Hochschule Mittelhessen, 35390, Giessen, Germany
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Chen XY, Sun HZ, Qiao B, Miao CH, Hou ZJ, Xu SJ, Xu QM, Cheng JS. Improved the lipopeptide production of Bacillus amyloliquefaciens HM618 under co-culture with the recombinant Corynebacterium glutamicum producing high-level proline. BIORESOURCE TECHNOLOGY 2022; 349:126863. [PMID: 35183721 DOI: 10.1016/j.biortech.2022.126863] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 02/13/2022] [Accepted: 02/14/2022] [Indexed: 06/14/2023]
Abstract
The application of antibacterial lipopeptides is limited by high cost and low yield. Herein, the exogenous L-proline significantly improved lipopeptide production by Bacillus amyloliquefaciens HM618. A recombinant Corynebacterium glutamicum producing high levels of proline using genetically modifying proB and putA was used to establish consortium, to improve lipopeptide production of strain HM618. Compared to a pure culture, the levels of iturin A, fengycin, and surfactin in consortium reached 67.75, 39.32, and 37.25 mg L-1, respectively, an increase of 3.19-, 2.05-, and 1.63-fold over that produced by co-cultures of B. amyloliquefaciens and recombinant C. glutamicum with normal medium. Commercial amylase and recombinant Pichia pastoris with a heterologous amylase gene were used to hydrolyze kitchen waste. A three-strain consortium with recombinant P. pastoris and C. glutamicum increased the lipopeptide production of strain HM618 in medium containing KW. This work provides new strategies to improve lipopeptide production by B. amyloliquefaciens.
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Affiliation(s)
- Xin-Yue Chen
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin 300350, PR China; SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin 300350, PR China
| | - Hui-Zhong Sun
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin 300350, PR China; SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin 300350, PR China
| | - Bin Qiao
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin 300350, PR China
| | - Chang-Hao Miao
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin 300350, PR China; SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin 300350, PR China
| | - Zheng-Jie Hou
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin 300350, PR China; SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin 300350, PR China
| | - Shu-Jing Xu
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin 300350, PR China; SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin 300350, PR China
| | - Qiu-Man Xu
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Science, Tianjin Normal University, Binshuixi Road 393, Xiqing District, Tianjin 300387, People's Republic of China
| | - Jing-Sheng Cheng
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin 300350, PR China; SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin 300350, PR China.
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11
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Virdis B, Hoelzle R, Marchetti A, Boto ST, Rosenbaum MA, Blasco-Gómez R, Puig S, Freguia S, Villano M. Electro-fermentation: Sustainable bioproductions steered by electricity. Biotechnol Adv 2022; 59:107950. [PMID: 35364226 DOI: 10.1016/j.biotechadv.2022.107950] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 02/22/2022] [Accepted: 03/24/2022] [Indexed: 01/06/2023]
Abstract
The market of biobased products obtainable via fermentation processes is steadily increasing over the past few years, driven by the need to create a decarbonized economy. To date, industrial fermentation (IF) employs either pure or mixed microbial cultures (MMC) whereby the type of the microbial catalysts and the used feedstock affect metabolic pathways and, in turn, the type of product(s) generated. In many cases, especially when dealing with MMC, the economic viability of IF is hindered by factors such as the low attained product titer and selectivity, which ultimately challenge the downstream recovery and purification steps. In this context, electro-fermentation (EF) represents an innovative approach, based on the use of a polarized electrode interface to trigger changes in the rate, yield, titer or product distribution deriving from traditional fermentation processes. In principle, the electrode in EF can act as an electron acceptor (i.e., anodic electro-fermentation, AEF) or donor (i.e., cathodic electro-fermentation, CEF), or simply as a mean to control the oxidation-reduction potential of the fermentation broth. However, the molecular and biochemical basis underlying the EF process are still largely unknown. This review paper provides a comprehensive overview of recent literature studies including both AEF and CEF examples with either pure or mixed microbial cultures. A critical analysis of biochemical, microbiological, and engineering aspects which presently hamper the transition of the EF technology from the laboratory to the market is also presented.
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Affiliation(s)
- Bernardino Virdis
- Australian Centre for Water and Environmental Biotechnology (ACWEB, formerly AWMC), The University of Queensland, Brisbane, QLD 4072, Australia
| | - Robert Hoelzle
- School of Earth and Environmental Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Angela Marchetti
- Department of Chemistry, Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Santiago T Boto
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute (HKI), 07745 Jena, Germany; Faculty of Biological Sciences, Friedrich Schiller University (FSU), 07743 Jena, Germany
| | - Miriam A Rosenbaum
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute (HKI), 07745 Jena, Germany; Faculty of Biological Sciences, Friedrich Schiller University (FSU), 07743 Jena, Germany
| | - Ramiro Blasco-Gómez
- LEQUIA, Institute of the Environment, University of Girona, Maria Aurèlia Capmany 69, 17003 Girona, Spain
| | - Sebastià Puig
- LEQUIA, Institute of the Environment, University of Girona, Maria Aurèlia Capmany 69, 17003 Girona, Spain
| | - Stefano Freguia
- Department of Chemical Engineering, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Marianna Villano
- Department of Chemistry, Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy.
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12
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Han P, Teo WZ, Yew WS. Biologically engineered microbes for bioremediation of electronic waste: Wayposts, challenges and future directions. ENGINEERING BIOLOGY 2022; 6:23-34. [PMID: 36968558 PMCID: PMC9995160 DOI: 10.1049/enb2.12020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 01/17/2022] [Accepted: 02/21/2022] [Indexed: 12/25/2022] Open
Abstract
In the face of a burgeoning stream of e-waste globally, e-waste recycling becomes increasingly imperative, not only to mitigate the environmental and health risks it poses but also as an urban mining strategy for resource recovery of precious metals, rare Earth elements, and even plastics. As part of the continual efforts to develop greener alternatives to conventional approaches of e-waste recycling, biologically assisted degradation of e-waste offers a promising recourse by capitalising on certain microorganisms' innate ability to interact with metals or degrade plastics. By harnessing emerging genetic tools in synthetic biology, the evolution of novel or enhanced capabilities needed to advance bioremediation and resource recovery could be potentially accelerated by improving enzyme catalytic abilities, modifying substrate specificities, and increasing toxicity tolerance. Yet, the management of e-waste presents formidable challenges due to its massive volume, high component complexity, and associated toxicity. Several limitations will need to be addressed before nascent laboratory-scale achievements in bioremediation can be translated to viable industrial applications. Nonetheless, vested groups, involving both start-up and established companies, have taken visionary steps towards deploying microbes for commercial implementation in e-waste recycling.
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Affiliation(s)
- Ping Han
- Synthetic Biology for Clinical and Technological InnovationNational University of SingaporeSingaporeSingapore
- Synthetic Biology Translational Research ProgrammeYong Loo Lin School of MedicineNational University of SingaporeSingaporeSingapore
- Department of BiochemistryYong Loo Lin School of MedicineNational University of SingaporeSingaporeSingapore
| | - Wei Zhe Teo
- Synthetic Biology for Clinical and Technological InnovationNational University of SingaporeSingaporeSingapore
- Synthetic Biology Translational Research ProgrammeYong Loo Lin School of MedicineNational University of SingaporeSingaporeSingapore
- Department of BiochemistryYong Loo Lin School of MedicineNational University of SingaporeSingaporeSingapore
| | - Wen Shan Yew
- Synthetic Biology for Clinical and Technological InnovationNational University of SingaporeSingaporeSingapore
- Synthetic Biology Translational Research ProgrammeYong Loo Lin School of MedicineNational University of SingaporeSingaporeSingapore
- Department of BiochemistryYong Loo Lin School of MedicineNational University of SingaporeSingaporeSingapore
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13
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Hussain MH, Mohsin MZ, Zaman WQ, Yu J, Zhao X, Wei Y, Zhuang Y, Mohsin A, Guo M. Multiscale engineering of microbial cell factories: A step forward towards sustainable natural products industry. Synth Syst Biotechnol 2022; 7:586-601. [PMID: 35155840 PMCID: PMC8816652 DOI: 10.1016/j.synbio.2021.12.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 12/08/2021] [Accepted: 12/30/2021] [Indexed: 01/09/2023] Open
Abstract
Microbial cell factories (bacteria and fungi) are the leading producers of beneficial natural products such as lycopene, carotene, herbal medicine, and biodiesel etc. These microorganisms are considered efficient due to their effective bioprocessing strategy (monoculture- and consortial-based approach) under distinct processing conditions. Meanwhile, the advancement in genetic and process optimization techniques leads to enhanced biosynthesis of natural products that are known functional ingredients with numerous applications in the food, cosmetic and medical industries. Natural consortia and monoculture thrive in nature in a small proportion, such as wastewater, food products, and soils. In similitude to natural consortia, it is possible to engineer artificial microbial consortia and program their behaviours via synthetic biology tools. Therefore, this review summarizes the optimization of genetic and physicochemical parameters of the microbial system for improved production of natural products. Also, this review presents a brief history of natural consortium and describes the functional properties of monocultures. This review focuses on synthetic biology tools that enable new approaches to design synthetic consortia; and highlights the syntropic interactions that determine the performance and stability of synthetic consortia. In particular, the effect of processing conditions and advanced genetic techniques to improve the productibility of both monoculture and consortial based systems have been greatly emphasized. In this context, possible strategies are also discussed to give an insight into microbial engineering for improved production of natural products in the future. In summary, it is concluded that the coupling of genomic modifications with optimum physicochemical factors would be promising for producing a robust microbial cell factory that shall contribute to the increased production of natural products.
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Affiliation(s)
- Muhammad Hammad Hussain
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, PR China
| | - Muhammad Zubair Mohsin
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, PR China
| | - Waqas Qamar Zaman
- Institute of Environmental Sciences and Engineering, School of Civil and Environmental Engineering, National University of Sciences and Technology (NUST), Sector H-12, Islamabad, 44000, Pakistan
| | - Junxiong Yu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, PR China
| | - Xueli Zhao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, PR China
| | - Yanlong Wei
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, PR China
| | - Yingping Zhuang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, PR China
| | - Ali Mohsin
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, PR China
- Corresponding author. East China University of Science and Technology, 130 Meilong Rd, Shanghai, 200237, PR China.
| | - Meijin Guo
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, PR China
- Corresponding author. P.O. box 329#, East China University of Science and Technology, 130 Meilong Rd., Shanghai, 200237, PR China.
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Diffusion-controlled release of the theranostic protein-photosensitizer Azulitox from composite of Fmoc-Phenylalanine Fibrils encapsulated with BSA hydrogels. J Biotechnol 2021; 341:51-62. [PMID: 34464649 DOI: 10.1016/j.jbiotec.2021.08.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 08/06/2021] [Accepted: 08/25/2021] [Indexed: 12/21/2022]
Abstract
Hydrogels offer a promising potential for the encapsulation and regulated release of drugs due to their biocompatibility and their tunable properties as materials. Only a limited number of systems and procedures enable the encapsulation of sensitive proteins. N-terminally fmoc-protected phenylalanine has been shown to self-assemble into a transparent, stable hydrogel It can be considered a supergelator due to the low amount of monomers necessary for hydrogelation (0.1% w/v), making it a good candidate for the encapsulation and stabilization of sensitive proteins. However, application options for this hydrogel are rather limited to those of many other fibril-based materials due to its intrinsic lack of mechanical strength and high susceptibility to changes in environmental conditions. Here, we demonstrate that the stability of a fibrillary system and the resulting release of the protein-photosensitizer Azulitox can be increased by combining the hydrogel with a tightly cross-linked BSA hydrogel. Azulitox is known to display cell-penetrating properties, anti-proliferative activity and has a distinctive fluorescence. Confocal microscopy and fluorescence measurements verified the maintenance of all essential functions of the encapsulated protein. In contrast, the combination of fibrillary and protein hydrogel resulted in a significant stabilization of the matrix and an adjustable release pattern for encapsulated protein.
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Giannari D, Ho CH, Mahadevan R. A gap-filling algorithm for prediction of metabolic interactions in microbial communities. PLoS Comput Biol 2021; 17:e1009060. [PMID: 34723959 PMCID: PMC8584699 DOI: 10.1371/journal.pcbi.1009060] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 11/11/2021] [Accepted: 10/05/2021] [Indexed: 11/24/2022] Open
Abstract
The study of microbial communities and their interactions has attracted the interest of the scientific community, because of their potential for applications in biotechnology, ecology and medicine. The complexity of interspecies interactions, which are key for the macroscopic behavior of microbial communities, cannot be studied easily experimentally. For this reason, the modeling of microbial communities has begun to leverage the knowledge of established constraint-based methods, which have long been used for studying and analyzing the microbial metabolism of individual species based on genome-scale metabolic reconstructions of microorganisms. A main problem of genome-scale metabolic reconstructions is that they usually contain metabolic gaps due to genome misannotations and unknown enzyme functions. This problem is traditionally solved by using gap-filling algorithms that add biochemical reactions from external databases to the metabolic reconstruction, in order to restore model growth. However, gap-filling algorithms could evolve by taking into account metabolic interactions among species that coexist in microbial communities. In this work, a gap-filling method that resolves metabolic gaps at the community level was developed. The efficacy of the algorithm was tested by analyzing its ability to resolve metabolic gaps on a synthetic community of auxotrophic Escherichia coli strains. Subsequently, the algorithm was applied to resolve metabolic gaps and predict metabolic interactions in a community of Bifidobacterium adolescentis and Faecalibacterium prausnitzii, two species present in the human gut microbiota, and in an experimentally studied community of Dehalobacter and Bacteroidales species of the ACT-3 community. The community gap-filling method can facilitate the improvement of metabolic models and the identification of metabolic interactions that are difficult to identify experimentally in microbial communities.
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Affiliation(s)
- Dafni Giannari
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | | | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
- The Institute of Biomaterials & Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
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16
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Mathematical Analysis and Update of ADM1 Model for Biomethane Production by Anaerobic Digestion. FERMENTATION 2021. [DOI: 10.3390/fermentation7040237] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Biomethane is a renewable product that can directly substitute its fossil counterpart, although its synthesis from residual biomasses has some hurdles. Because of the complex nature of both biomasses and the microbial consortia involved, innovative approaches such as mathematical modeling can be deployed to support possible improvements. The goal of this study is two-fold, as we aimed to modify a part of the Anaerobic Digestion Model No. 1 (ADM1), describing biomethane production from activated sludge, matching with its actual microbial nature, and to use the model for identifying relevant parameters to improve biomethane production. Firstly, thermodynamic analysis was performed, highlighting the direct route from glucose to biomethane as the most favorable. Then, by using MATLAB® and Simulink Toolbox, we discovered that the model fails to predict the microbiological behavior of the system. The structure of the ADM1 model was then modified by adding substrate consumption yields in equations describing microbial growth, to better reflect the consortium behavior. The updated model was tested by modifying several parameters: the coefficient of decomposition was identified to increase biomethane production. Approaching mathematical models from a microbiological point of view can lead to further improvement of the models themselves. Furthermore, this work represents additional evidence of the importance of informatics tools, such as bioprocess simulations to foster biomethane role in bioeconomy.
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17
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Ballerstedt H, Tiso T, Wierckx N, Wei R, Averous L, Bornscheuer U, O’Connor K, Floehr T, Jupke A, Klankermayer J, Liu L, de Lorenzo V, Narancic T, Nogales J, Perrin R, Pollet E, Prieto A, Casey W, Haarmann T, Sarbu A, Schwaneberg U, Xin F, Dong W, Xing J, Chen GQ, Tan T, Jiang M, Blank LM. MIXed plastics biodegradation and UPcycling using microbial communities: EU Horizon 2020 project MIX-UP started January 2020. ENVIRONMENTAL SCIENCES EUROPE 2021; 33:99. [PMID: 34458054 PMCID: PMC8380104 DOI: 10.1186/s12302-021-00536-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 07/31/2021] [Indexed: 05/16/2023]
Abstract
This article introduces the EU Horizon 2020 research project MIX-UP, "Mixed plastics biodegradation and upcycling using microbial communities". The project focuses on changing the traditional linear value chain of plastics to a sustainable, biodegradable based one. Plastic mixtures contain five of the top six fossil-based recalcitrant plastics [polyethylene (PE), polyurethane (PUR), polypropylene (PP), polyethylene terephthalate (PET), polystyrene (PS)], along with upcoming bioplastics polyhydroxyalkanoate (PHA) and polylactate (PLA) will be used as feedstock for microbial transformations. Consecutive controlled enzymatic and microbial degradation of mechanically pre-treated plastics wastes combined with subsequent microbial conversion to polymers and value-added chemicals by mixed cultures. Known plastic-degrading enzymes will be optimised by integrated protein engineering to achieve high specific binding capacities, stability, and catalytic efficacy towards a broad spectrum of plastic polymers under high salt and temperature conditions. Another focus lies in the search and isolation of novel enzymes active on recalcitrant polymers. MIX-UP will formulate enzyme cocktails tailored to specific waste streams and strives to enhance enzyme production significantly. In vivo and in vitro application of these cocktails enable stable, self-sustaining microbiomes to convert the released plastic monomers selectively into value-added products, key building blocks, and biomass. Any remaining material recalcitrant to the enzymatic activities will be recirculated into the process by physicochemical treatment. The Chinese-European MIX-UP consortium is multidisciplinary and industry-participating to address the market need for novel sustainable routes to valorise plastic waste streams. The project's new workflow realises a circular (bio)plastic economy and adds value to present poorly recycled plastic wastes where mechanical and chemical plastic recycling show limits.
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Affiliation(s)
- Hendrik Ballerstedt
- Institute of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Till Tiso
- Institute of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Nick Wierckx
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Research Center Jülich, Wilhelm Johnen Straße, 52428 Jülich, Germany
| | - Ren Wei
- Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
| | - Luc Averous
- BioTeam/ICPEES-ECPM, UMR CNRS 7515, Université de Strasbourg, 25 rue Becquerel, 67087 Strasbourg Cedex 2, France
| | - Uwe Bornscheuer
- Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
| | - Kevin O’Connor
- BiOrbic Bioeconomy SFI Research Centre, UCD Earth Institute and School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Tilman Floehr
- everwave GmbH, Strüverweg 116, 52070 Aachen, Germany
| | - Andreas Jupke
- Fluid Process Engineering, Aachen Process Technology (AVT), RWTH Aachen University, Forckenbeckstraße 51, 52074 Aachen, Germany
| | - Jürgen Klankermayer
- Institute of Technical and Macromolecular Chemistry (ITMC), RWTH Aachen University, Worringerweg 2, 52074 Aachen, Germany
| | - Luo Liu
- College of Life Science and Technology (CLST), Beijing University of Chemical Technology, Beisanhuan EastRoad 15, Chaoyang District, Beijing, 100029 PR China
| | - Victor de Lorenzo
- Interdisciplinary Platform for Sustainable Plastics Towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Biological Research Center (CIB-CSIC), 28040 Madrid, Spain
| | - Tanja Narancic
- BiOrbic Bioeconomy SFI Research Centre, UCD Earth Institute and School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Juan Nogales
- Interdisciplinary Platform for Sustainable Plastics Towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Biological Research Center (CIB-CSIC), 28040 Madrid, Spain
| | - Rémi Perrin
- SOPREMA, Direction R&D, 14 Rue Saint Nazaire, 67100 Strasbourg, France
| | - Eric Pollet
- BioTeam/ICPEES-ECPM, UMR CNRS 7515, Université de Strasbourg, 25 rue Becquerel, 67087 Strasbourg Cedex 2, France
| | - Auxiliadora Prieto
- Interdisciplinary Platform for Sustainable Plastics Towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Biological Research Center (CIB-CSIC), 28040 Madrid, Spain
| | - William Casey
- Bioplastech Ltd., Nova UCD, Belfield Innovation Park, University College Dublin, Belfield, Dublin 4, Ireland
| | - Thomas Haarmann
- AB Enzymes GmbH, Feldbergstraße 78, 64293 Darmstadt, Germany
| | - Alexandru Sarbu
- SOPREMA, Direction R&D, 14 Rue Saint Nazaire, 67100 Strasbourg, France
| | - Ulrich Schwaneberg
- Institute of Biotechnology (BIOTEC), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Fengxue Xin
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 Puzhu Road, Nanjing, 211816 PR China
| | - Weiliang Dong
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 Puzhu Road, Nanjing, 211816 PR China
| | - Jiamin Xing
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering (IPE), Chinese Academy of Sciences, 1 North 2nd Street, Zhongguancun, Beijing, 100190 PR China
| | - Guo-Qiang Chen
- School of Life Sciences (SLS), Tsinghua University, Beijing, 100084 PR China
| | - Tianwei Tan
- College of Life Science and Technology (CLST), Beijing University of Chemical Technology, Beisanhuan EastRoad 15, Chaoyang District, Beijing, 100029 PR China
| | - Min Jiang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 Puzhu Road, Nanjing, 211816 PR China
| | - Lars M. Blank
- Institute of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
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Zhang J, Luo W, Wang Z, Chen X, Lv P, Xu J. A novel strategy for D-psicose and lipase co-production using a co-culture system of engineered Bacillus subtilis and Escherichia coli and bioprocess analysis using metabolomics. BIORESOUR BIOPROCESS 2021; 8:77. [PMID: 38650263 PMCID: PMC10992840 DOI: 10.1186/s40643-021-00429-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 08/11/2021] [Indexed: 11/10/2022] Open
Abstract
To develop an economically feasible fermentation process, this study designed a novel bioprocess based on the co-culture of engineered Bacillus subtilis and Escherichia coli for the co-production of extracellular D-psicose and intracellular lipase. After optimizing the co-culture bioprocess, 11.70 g/L of D-psicose along with 16.03 U/mg of lipase was obtained; the glucose and fructose were completely utilized. Hence, the conversion rate of D-psicose reached 69.54%. Compared with mono-culture, lipase activity increased by 58.24%, and D-psicose production increased by 7.08%. In addition, the co-culture bioprocess was explored through metabolomics analysis, which included 168 carboxylic acids and derivatives, 70 organooxygen compounds, 34 diazines, 32 pyridines and derivatives, 30 benzene and substituted derivatives, and other compounds. It also could be found that the relative abundance of differential metabolites in the co-culture system was significantly higher than that in the mono-culture system. Pathway analysis revealed that, tryptophan metabolism and β-alanine metabolism had the highest correlation and played an important role in the co-culture system; among them, tryptophan metabolism regulates protein synthesis and β-alanine metabolism, which is related to the formation of metabolic by-products. These results confirm that the co-cultivation of B. subtilis and E. coli can provide a novel idea for D-psicose and lipase biorefinery, and are beneficial for the discovery of valuable secondary metabolites such as turanose and morusin.
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Affiliation(s)
- Jun Zhang
- Guangdong Provincial Key Laboratory of New and Renewable Energy Research and Development, Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, CAS Key Laboratory of Renewable Energy, Guangzhou, 510640, China
- College of Food Science and Technology, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Provincial Engineering Technology Research Center of Seafood, Key Laboratory of Advanced Processing of Aquatic Product of Guangdong Higher Education Institution, Guangdong Ocean University, Zhanjiang, 524088 , China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wen Luo
- Guangdong Provincial Key Laboratory of New and Renewable Energy Research and Development, Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, CAS Key Laboratory of Renewable Energy, Guangzhou, 510640, China
| | - Zhiyuan Wang
- Guangdong Provincial Key Laboratory of New and Renewable Energy Research and Development, Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, CAS Key Laboratory of Renewable Energy, Guangzhou, 510640, China
| | - Xiaoyan Chen
- Guangdong Provincial Key Laboratory of New and Renewable Energy Research and Development, Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, CAS Key Laboratory of Renewable Energy, Guangzhou, 510640, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Pengmei Lv
- Guangdong Provincial Key Laboratory of New and Renewable Energy Research and Development, Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, CAS Key Laboratory of Renewable Energy, Guangzhou, 510640, China.
| | - Jingliang Xu
- Guangdong Provincial Key Laboratory of New and Renewable Energy Research and Development, Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, CAS Key Laboratory of Renewable Energy, Guangzhou, 510640, China.
- School of Chemical Engineering, Zhengzhou University, Zhengzhou, 450001 , China.
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19
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Leonov PS, Flores-Alsina X, Gernaey KV, Sternberg C. Microbial biofilms in biorefinery - Towards a sustainable production of low-value bulk chemicals and fuels. Biotechnol Adv 2021; 50:107766. [PMID: 33965529 DOI: 10.1016/j.biotechadv.2021.107766] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 04/11/2021] [Accepted: 05/04/2021] [Indexed: 12/14/2022]
Abstract
Harnessing the potential of biocatalytic conversion of renewable biomass into value-added products is still hampered by unfavorable process economics. This has promoted the use of biofilms as an alternative to overcome the limitations of traditional planktonic systems. In this paper, the benefits and challenges of biofilm fermentations are reviewed with a focus on the production of low-value bulk chemicals and fuels from waste biomass. Our study demonstrates that biofilm fermentations can potentially improve productivities and product yields by increasing biomass retention and allowing for continuous operation at high dilution rates. Furthermore, we show that biofilms can tolerate hazardous environments, which improve the conversion of crude biomass under substrate and product inhibitory conditions. Additionally, we present examples for the improved conversion of pure and crude substrates into bulk chemicals by mixed microbial biofilms, which can benefit from microenvironments in biofilms for synergistic multi-species reactions, and improved resistance to contaminants. Finally, we suggest the use of mathematical models as useful tools to supplement experimental insights related to the effects of physico-chemical and biological phenomena on the process. Major challenges for biofilm fermentations arise from inconsistent fermentation performance, slow reactor start-up, biofilm carrier costs and carrier clogging, insufficient biofilm monitoring and process control, challenges in reactor sterilization and scale-up, and issues in recovering dilute products. The key to a successful commercialization of the technology is likely going to be an interdisciplinary approach. Crucial research areas might include genetic engineering combined with the development of specialized biofilm reactors, biofilm carrier development, in-situ biofilm monitoring, model-based process control, mixed microbial biofilm technology, development of suitable biofilm reactor scale-up criteria, and in-situ product recovery.
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Affiliation(s)
- Pascal S Leonov
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 221, 2800 Kgs. Lyngby, Denmark; Department of Chemical and Biochemical Engineering, Technical University of Denmark, Søltofts Plads, Building 228 A, 2800 Kgs. Lyngby, Denmark
| | - Xavier Flores-Alsina
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Søltofts Plads, Building 228 A, 2800 Kgs. Lyngby, Denmark
| | - Krist V Gernaey
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Søltofts Plads, Building 228 A, 2800 Kgs. Lyngby, Denmark
| | - Claus Sternberg
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 221, 2800 Kgs. Lyngby, Denmark.
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Friends or Foes-Microbial Interactions in Nature. BIOLOGY 2021; 10:biology10060496. [PMID: 34199553 PMCID: PMC8229319 DOI: 10.3390/biology10060496] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 05/27/2021] [Accepted: 05/31/2021] [Indexed: 12/16/2022]
Abstract
Simple Summary Microorganisms like bacteria, archaea, fungi, microalgae, and viruses mostly form complex interactive networks within the ecosystem rather than existing as single planktonic cells. Interactions among microorganisms occur between the same species, with different species, or even among entirely different genera, families, or even domains. These interactions occur after environmental sensing, followed by converting those signals to molecular and genetic information, including many mechanisms and classes of molecules. Comprehensive studies on microbial interactions disclose key strategies of microbes to colonize and establish in a variety of different environments. Knowledge of the mechanisms involved in the microbial interactions is essential to understand the ecological impact of microbes and the development of dysbioses. It might be the key to exploit strategies and specific agents against different facing challenges, such as chronic and infectious diseases, hunger crisis, pollution, and sustainability. Abstract Microorganisms are present in nearly every niche on Earth and mainly do not exist solely but form communities of single or mixed species. Within such microbial populations and between the microbes and a eukaryotic host, various microbial interactions take place in an ever-changing environment. Those microbial interactions are crucial for a successful establishment and maintenance of a microbial population. The basic unit of interaction is the gene expression of each organism in this community in response to biotic or abiotic stimuli. Differential gene expression is responsible for producing exchangeable molecules involved in the interactions, ultimately leading to community behavior. Cooperative and competitive interactions within bacterial communities and between the associated bacteria and the host are the focus of this review, emphasizing microbial cell–cell communication (quorum sensing). Further, metagenomics is discussed as a helpful tool to analyze the complex genomic information of microbial communities and the functional role of different microbes within a community and to identify novel biomolecules for biotechnological applications.
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21
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D'Hondt K, Kostic T, McDowell R, Eudes F, Singh BK, Sarkar S, Markakis M, Schelkle B, Maguin E, Sessitsch A. Microbiome innovations for a sustainable future. Nat Microbiol 2021; 6:138-142. [PMID: 33510435 DOI: 10.1038/s41564-020-00857-w] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Kathleen D'Hondt
- Department of Economy, Science and Innovation - Flemish Government, Brussels, Belgium
| | - Tanja Kostic
- Bioresources Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Richard McDowell
- AgResearch, Lincoln Science Centre, Christchurch, New Zealand.,Faculty of Agriculture and Life Sciences, Lincoln University, Christchurch, New Zealand
| | - Francois Eudes
- Lethbridge Research and Development Centre, Science and Technology Branch, Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada
| | - Brajesh K Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia.,Global Centre for Land-Based Innovation, Western Sydney University, Penrith, New South Wales, Australia
| | - Sara Sarkar
- International Engagement Division, Science and Technology Branch, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Marios Markakis
- Bioeconomy & Food Systems Unit, Healthy Planet Directorate, Directorate-General for Research and Innovation, European Commission, Brussels, Belgium
| | | | - Emmanuelle Maguin
- UMR1319 MICALIS, Université Paris Saclay, INRAE, AgroParisTech, Jouy-en-Josas, France
| | - Angela Sessitsch
- Bioresources Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria.
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22
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Enrichment of Hydrogen Oxidizing Bacteria from High Temperature and Salinity Environments. Appl Environ Microbiol 2021; 87:AEM.02439-20. [PMID: 33257312 PMCID: PMC7851685 DOI: 10.1128/aem.02439-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
There is an urgent need for sustainable protein supply routes with low environmental footprint. Recently, the use of hydrogen oxidizing bacteria (HOB) as a platform for high quality microbial protein (MP) production has regained interest. This study aims to investigate the added value of using conditions such as salt and temperature to steer HOB communities to lower diversities, while maintaining a high protein content and a high quality amino acid profile. Pressure drop and hydrogen consumption were measured for 56 days to evaluate autotrophy of a total of six communities in serum flasks. Of the six communities, four were enriched under saline (0.0, 0.25, 0.5 and 1.0 mol NaCl l-1) and two under thermophilic conditions (65°C). Five communities enriched for HOB were subsequently cultivated in continuously stirred reactors under the same conditions to evaluate their potential as microbial protein producers. The protein percentages ranged from 41 to 80%. The highest protein content was obtained for the thermophilic enrichments. Amino acid profiles were comparable to protein sources commonly used for feed purposes. Members of the genus Achromobacter were found to dominate the saline enrichments while members of the genus Hydrogenibacillus were found to dominate the thermophilic enrichments. Here we show that enriching for HOB while steering the community toward low diversity and maintaining a high quality protein content can be successfully achieved, both in saline and thermophilic conditions.IMPORTANCE Alternative feed and food supply chains are required to decrease water and land use. HOB offer a promising substitute for traditional agricultural practice to produce microbial protein (MP) from residual materials and renewable energy. To safeguard product stability, the composition of the HOB community should be controlled. Defining strategies to maintain the stability of the communities is therefore key for optimization purposes. In this study, we use salt and temperature as independent conditions to stabilize the composition of the HOB communities. Based on the results presented, we conclude that HOB communities can be steered to have low diversity using the presented conditions while producing a desirable protein content with a valuable amino acid profile.
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Jiang LL, Liu FY, Yang W, Li CL, Zhu BW, Zhu XH. Production of 1,3-propanediol and lactic acid from crude glycerol by a microbial consortium from intertidal sludge. Biotechnol Lett 2021; 43:711-717. [PMID: 33386498 DOI: 10.1007/s10529-020-03063-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 12/12/2020] [Indexed: 12/01/2022]
Abstract
OBJECTIVES To select a microbial consortium from intertidal sludge and evaluate its ability to convert crude glycerol from biodisel to high value-added products such as 1,3-propanediol (1,3-PDO) and lactic acid (LA). RESULTS A microbial consortium named CJD-S was selected from intertidal sludge and exhibited excellent performance for the conversion of crude glycerol to 1,3-PDO and LA. The composition of CJD-S was determined to be 85.99% Enterobacteriaceae and 13.75% Enterococcaceae by 16S rRNA gene amplicon high-throughput sequencing. In fed-batch fermentation with crude glycerol under nonsterile conditions, the highest concentrations of 1,3-PDO and LA were 41.47 g/L and 45.86 g/L, respectively. CONCLUSIONS The selected microbial consortium, CJD-S, effectively converted crude glycerol to 1,3-PDO and LA under nonsterile conditions and can contribute to the sustainable development of the biodiesel industry.
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Affiliation(s)
- Li-Li Jiang
- School of Chemical and Environmental Engineering, Yingkou Institute of Technology, Yingkou, 115014, Liaoning Province, China. .,Jiangsu Key Laboratory for Biomass Energy and Material, Nanjing, 210042, Jiangsu Province, China. .,Liaoning Key Laboratory of Additive Synthesis and Separation, Yingkou Institute of Technology, Yingkou, 115014, Liaoning Province, China.
| | - Feng-Yi Liu
- School of Chemical and Environmental Engineering, Yingkou Institute of Technology, Yingkou, 115014, Liaoning Province, China
| | - Wei Yang
- School of Chemical and Environmental Engineering, Yingkou Institute of Technology, Yingkou, 115014, Liaoning Province, China
| | - Chang-Li Li
- School of Chemical and Environmental Engineering, Yingkou Institute of Technology, Yingkou, 115014, Liaoning Province, China.,Liaoning Key Laboratory of Additive Synthesis and Separation, Yingkou Institute of Technology, Yingkou, 115014, Liaoning Province, China
| | - Bao-Wei Zhu
- School of Chemical and Environmental Engineering, Yingkou Institute of Technology, Yingkou, 115014, Liaoning Province, China
| | - Xiu-Hui Zhu
- School of Chemical and Environmental Engineering, Yingkou Institute of Technology, Yingkou, 115014, Liaoning Province, China.,Liaoning Key Laboratory of Additive Synthesis and Separation, Yingkou Institute of Technology, Yingkou, 115014, Liaoning Province, China
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24
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Changes in freshwater sediment microbial populations during fermentation of crude glycerol. ELECTRON J BIOTECHN 2021. [DOI: 10.1016/j.ejbt.2020.10.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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25
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Albright MBN, Sevanto S, Gallegos-Graves LV, Dunbar J. Biotic Interactions Are More Important than Propagule Pressure in Microbial Community Invasions. mBio 2020; 11:e02089-20. [PMID: 33109758 PMCID: PMC7593967 DOI: 10.1128/mbio.02089-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 10/07/2020] [Indexed: 01/08/2023] Open
Abstract
Microbial probiotics are intended to improve functions in diverse ecosystems, yet probiotics often fail to establish in a preexisting microbiome. This is a species invasion problem. The relative importance of the two major factors controlling establishment in this context-propagule pressure (inoculation dose and frequency) and biotic interactions (composition of introduced and resident communities)-is unknown. We tested the effect of these factors in driving microbial composition and functioning following 12 microbial community invasions (e.g., introductions of many microbial invaders) in microcosms. Ecosystem functioning over a 30-day postinvasion period was assessed by measuring activity (respiration) and environment modification (dissolved organic carbon abundance). To test the dependence on environmental context, experiments were performed in two resource environments. In both environments, biotic interactions were more important than propagule pressure in driving microbial composition and community function, but the magnitude of effect varied by environment. Successful invaders comprised approximately 8% of the total number of operational taxonomic units (OTUs). Bacteria were better invaders than fungi, with average relative abundances of 7.4% ± 6.8% and 1.5% ± 1.4% of OTUs, respectively. Common bacterial invaders were associated with stress response traits. The most resilient bacterial and fungal families, in other words, those least impacted by invasions, were linked to antimicrobial resistance or production traits. Illuminating the principles that determine community composition and functioning following microbial invasions is key to efficient community engineering.IMPORTANCE With increasing frequency, humans are introducing new microbes into preexisting microbiomes to alter functioning. Example applications include modification of microflora in human guts for better health and those of soil for food security and/or climate management. Probiotic applications are often approached as trial-and-error endeavors and have mixed outcomes. We propose that increased success in microbiome engineering may be achieved with a better understanding of microbial invasions. We conducted a microbial community invasion experiment to test the relative importance of propagule pressure and biotic interactions in driving microbial community composition and ecosystem functioning in microcosms. We found that biotic interactions were more important than propagule pressure in determining the impact of microbial invasions. Furthermore, the principles for community engineering vary among organismal groups (bacteria versus fungi).
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Affiliation(s)
| | - Sanna Sevanto
- Earth and Environmental Sciences Division, Los Alamos National Laboratory, Los Alamos, New Mexico
| | | | - John Dunbar
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico
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De Vrieze J, De Mulder T, Matassa S, Zhou J, Angenent LT, Boon N, Verstraete W. Stochasticity in microbiology: managing unpredictability to reach the Sustainable Development Goals. Microb Biotechnol 2020; 13:829-843. [PMID: 32311222 PMCID: PMC7264747 DOI: 10.1111/1751-7915.13575] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 03/04/2020] [Accepted: 03/25/2020] [Indexed: 01/06/2023] Open
Abstract
Pure (single) cultures of microorganisms and mixed microbial communities (microbiomes) have been important for centuries in providing renewable energy, clean water and food products to human society and will continue to play a crucial role to pursue the Sustainable Development Goals. To use microorganisms effectively, microbial engineered processes require adequate control. Microbial communities are shaped by manageable deterministic processes, but also by stochastic processes, which can promote unforeseeable variations and adaptations. Here, we highlight the impact of stochasticity in single culture and microbiome engineering. First, we discuss the concepts and mechanisms of stochasticity in relation to microbial ecology of single cultures and microbiomes. Second, we discuss the consequences of stochasticity in relation to process performance and human health, which are reflected in key disadvantages and important opportunities. Third, we propose a suitable decision tool to deal with stochasticity in which monitoring of stochasticity and setting the boundaries of stochasticity by regulators are central aspects. Stochasticity may give rise to some risks, such as the presence of pathogens in microbiomes. We argue here that by taking the necessary precautions and through clever monitoring and interpretation, these risks can be mitigated.
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Affiliation(s)
- Jo De Vrieze
- Center for Microbial Ecology and Technology (CMET), Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000, Gent, Belgium
| | | | - Silvio Matassa
- Department of Civil, Architectural and Environmental Engineering, University of Naples Federico II, via Claudio 21, 80125, Naples, Italy
| | - Jizhong Zhou
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
| | - Largus T Angenent
- Center for Applied Geosciences, University of Tübingen, Tübingen, Germany
| | - Nico Boon
- Center for Microbial Ecology and Technology (CMET), Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000, Gent, Belgium
| | - Willy Verstraete
- Center for Microbial Ecology and Technology (CMET), Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000, Gent, Belgium
- Avecom NV, Industrieweg 122P, Wondelgem, 9032, Belgium
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Wu W, Li X, Zhang X, Gu T, Qiu Y, Zhu M, Tan W. Characteristics of oxidative stress and antioxidant defenses by a mixed culture of acidophilic bacteria in response to Co 2+ exposure. Extremophiles 2020; 24:485-499. [PMID: 32322992 DOI: 10.1007/s00792-020-01170-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Accepted: 04/08/2020] [Indexed: 11/25/2022]
Abstract
During bioleaching of Cobalt from waste lithium-ion batteries, the biooxidation activity of acidophilic bacteria is inhibited by a high concentration of Co ion in the liquid phase. However, the mechanism for Co2+ toxicity to acidophilic bacteria has not been fully elucidated. In this study, the effects of Co2+ concentration on the biooxidation activity for Fe2+, intracellular reactive oxygen species (ROS) level and antioxidant defense systems in a mixed-culture of acidophilic bacteria (MCAB) were investigated. The results showed that the biooxidation activity of the MCAB was inhibited by Co2+. Furthermore, it was indicated that the intracellular ROS contents of the MCAB under conditions of 0.4 M and 0.6 M Co2+ were 2.60 and 3.34 times higher than that under the condition of 0 M Co2+. The increase in intracellular malondialdehyde content indicated that the oxidative damage was induced by Co2+. Moreover, the antioxidant systems in MCAB were affected by Co2+. It was observed that the Co2+ exposure increased the catalase and glutathione peroxidase activities while reducing the superoxide dismutase activity and the intracellular glutathione (GSH) content. It was found that an exogenous GSH supplementation eliminated excess intracellular ROS and improved the biooxidation activity of the MCAB.
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Affiliation(s)
- Weijin Wu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Xiyan Li
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Xu Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China.
| | - Tingyue Gu
- Department of Chemical and Biomolecular Engineering, Ohio University, Athens, OH, 45701, USA
| | - Yongqiu Qiu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Minglong Zhu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Wensong Tan
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China.
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28
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Ubando AT, Felix CB, Chen WH. Biorefineries in circular bioeconomy: A comprehensive review. BIORESOURCE TECHNOLOGY 2020; 299:122585. [PMID: 31901305 DOI: 10.1016/j.biortech.2019.122585] [Citation(s) in RCA: 179] [Impact Index Per Article: 44.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 12/05/2019] [Accepted: 12/06/2019] [Indexed: 05/23/2023]
Abstract
Biorefinery is a sustainable means of generating multiple bioenergy products from various biomass feedstocks through the incorporation of relevant conversion technologies. With the increased attention of circular economy in the past half-decade with the emphasis of holistically addressing economic, environmental, and social aspects of the industrial-sector, biorefinery acts as a strategic mechanism for the realization of a circular bioeconomy. This study presents a comprehensive review of different biorefinery models used for various biomass feedstocks such as lignocelluloses, algae, and numerous waste-types. The review focuses on how biorefinery is instrumental in the transition of various biomass-based industries in a circular bioeconomy. The results reveal that the social-economic aspect of the industrial sector has a major influence on the full adoption of biorefineries in circular bioeconomy. Biomass wastes have played a major role in the implementation of biorefinery in circular bioeconomy. The current challenges are also presented along with future perspectives.
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Affiliation(s)
- Aristotle T Ubando
- Department of Aeronautics and Astronautics, National Cheng Kung University, Tainan 701, Taiwan; Mechanical Engineering Department, De La Salle University, 2401 Taft Avenue, 0922 Manila, Philippines
| | - Charles B Felix
- Mechanical Engineering Department, De La Salle University, 2401 Taft Avenue, 0922 Manila, Philippines
| | - Wei-Hsin Chen
- Department of Aeronautics and Astronautics, National Cheng Kung University, Tainan 701, Taiwan; Department of Chemical and Materials Engineering, College of Engineering, Tunghai University, Taichung 407, Taiwan; Department of Mechanical Engineering, National Chin-Yi University of Technology, Taichung 411, Taiwan; Research Center for Energy Technology and Strategy, National Cheng Kung University, Tainan 701, Taiwan.
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29
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Sgobba E, Wendisch VF. Synthetic microbial consortia for small molecule production. Curr Opin Biotechnol 2019; 62:72-79. [PMID: 31627138 DOI: 10.1016/j.copbio.2019.09.011] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 09/06/2019] [Accepted: 09/11/2019] [Indexed: 11/26/2022]
Abstract
Microbial consortia were designed for the production of small molecules with 'labor' being divided between two or more microorganisms. Examples of linear designs are substrate conversion preceding target molecule production or subdivision of two consecutive steps of target molecule production. Here, we review synthetic biology design approaches for microbial consortia based on ecological principles and microbial interactions that is, mutualism, and commensalism. Besides highlighting the technical challenges regarding industrial application of synthetic microbial consortia, we forecast the extension of the concept from binary linear to ternary linear and more complex microbial consortia in biotechnological applications. Microbial consortia are here reviewed and proposed as a rational solution toward feedstock accessibility as it has been shown for production of l-lysine, l-pipecolic acid and cadaverine from starch or production of fumarate from microcrystalline cellulose and alkaline pre-treated corn, or alternatively to establish new multi-step pathway for the production of rosmarinic acid from xylose and glucose.
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Affiliation(s)
- Elvira Sgobba
- Genetics of Prokaryotes, Faculty of Biology and CeBiTec, Bielefeld University Bielefeld, Germany
| | - Volker F Wendisch
- Genetics of Prokaryotes, Faculty of Biology and CeBiTec, Bielefeld University Bielefeld, Germany.
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30
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Enriched hydrogen-oxidizing microbiomes show a high diversity of co-existing hydrogen-oxidizing bacteria. Appl Microbiol Biotechnol 2019; 103:8241-8253. [PMID: 31482282 DOI: 10.1007/s00253-019-10082-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 07/26/2019] [Accepted: 08/16/2019] [Indexed: 12/22/2022]
Abstract
While numerous reports exist on the axenic culturing of different hydrogen-oxidizing bacteria (HOB), knowledge about the enrichment of microbial communities growing on hydrogen, oxygen, and carbon dioxide as sole carbon and energy sources remains negligible. We want to elucidate if in such enrichments, most enriched populations are HOBs or heterotrophic organisms. In the present study, bacteria enriched from a soil sample and grown over 5 transfers using a continuous supply of hydrogen, oxygen, and carbon dioxide to obtain an enriched autotrophic hydrogen-oxidizing microbiome. The success of the enrichment was evaluated by monitoring ammonium consumption and biomass concentration for 120 days. The shift in the microbial composition of the original soil inoculum and all transfers was observed based on 16S rRNA amplicon sequencing. The hydrogen-oxidizing facultative chemolithoautotroph Hydrogenophaga electricum was isolated and found to be one of the abundant species in most transfers. Moreover, Achromobacter was isolated both under heterotrophic and autotrophic conditions, which was characterized as a hydrogen-oxidizing bacterium. The HOB enrichment condition constructed in this study provided an environment for HOB to develop and conquer in all transfers. In conclusion, we showed that enrichments on hydrogen, oxygen, and carbon dioxide as sole carbon and energy sources contain a diverse mixture of HOB and heterotrophs that resulted in a collection of culturable isolates. These isolates can be useful for further investigation for industrial applications.
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Sun Y, Zheng Y, Wang X, Zhou J, Xiu Z. Fermentation performance and mechanism of a novel microbial consortium DUT08 for 1,3-propandiol production from biodiesel-derived crude glycerol under non-strictly anaerobic conditions. Process Biochem 2019. [DOI: 10.1016/j.procbio.2019.05.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Wang XL, Zhou JJ, Sun YQ, Xiu ZL. Bioconversion of Raw Glycerol From Waste Cooking-Oil-Based Biodiesel Production to 1,3-Propanediol and Lactate by a Microbial Consortium. Front Bioeng Biotechnol 2019; 7:14. [PMID: 30834245 PMCID: PMC6387908 DOI: 10.3389/fbioe.2019.00014] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 01/18/2019] [Indexed: 01/04/2023] Open
Abstract
Waste cooking oil (WCO) is a sustainable alternative to raw vegetable oils and fats for biodiesel production considering both environmental and economic benefits. Raw glycerol from WCO-based biodiesel production (GWCO) is difficult to utilize via biological method, as multiple toxic impurities have inhibitory effects on microbial growth especially for pure cultures. In this work, four microbial consortia were selected from activated sludge by 30 serial transfers under different conditions. The obtained consortia exhibited lower diversity and species difference with the transfers. The consortium LS30 exhibited unique advantages for bioconversion of GWCO to 1,3-propanediol (1,3-PDO) and lactate (LA). Moreover, the fermentation could be performed economically under microaerobic and non-sterile conditions. The consortium consisted of 57.97% Enterobacter and 39.25% Escherichia could effectively convert 60 g/L GWCO to 1,3-PDO and LA in batch fermentation. In addition, this consortium exhibited better tolerance to fatty acid-derived crude glycerol (100 g/L), which demonstrated that specific toxic impurities in GWCO did pose a great challenge to microbial growth and metabolism. In fed batch fermentation, 27.77 g/L 1,3-PDO and 14.68 g/L LA were achieved. Compared with the consortium, a long lag phase in cell growth associated with a decreased glycerol consumption was observed in four single-strain fermentations. Furthermore, neither the consortium DL38 with excellent glycerol tolerance nor consortium C2-2M with high yield of 1,3-PDO could effectively transform GWCO into valuable products. The results demonstrated that the selected microbial consortium has the advanced adaptability to the toxic impurities in GWCO compared with other reported consortia and isolated single strain. This process can contribute to added-value use of GWCO.
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Affiliation(s)
| | | | | | - Zhi-Long Xiu
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, China
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33
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Stability and oscillatory behavior of microbial consortium in continuous conversion of crude glycerol to 1,3-propanediol. Appl Microbiol Biotechnol 2018; 102:8291-8305. [DOI: 10.1007/s00253-018-9244-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Revised: 06/29/2018] [Accepted: 07/13/2018] [Indexed: 10/28/2022]
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Sgobba E, Stumpf AK, Vortmann M, Jagmann N, Krehenbrink M, Dirks-Hofmeister ME, Moerschbacher B, Philipp B, Wendisch VF. Synthetic Escherichia coli-Corynebacterium glutamicum consortia for l-lysine production from starch and sucrose. BIORESOURCE TECHNOLOGY 2018; 260:302-310. [PMID: 29631180 DOI: 10.1016/j.biortech.2018.03.113] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Revised: 03/24/2018] [Accepted: 03/26/2018] [Indexed: 06/08/2023]
Abstract
In the biorefinery concept renewable feedstocks are converted to a multitude of value-added compounds irrespective of seasonal or other variations of the complex biomass substrates. Conceptionally, this can be realized by specialized single microbial strains or by co-culturing various strain combinations. In the latter approach strains for substrate conversion and for product formation can be combined. This study addressed the construction of binary microbial consortia based on starch- and sucrose-based production of l-lysine and derived value-added compounds. A commensalism-based synthetic consortium for l-lysine production from sucrose was developed combining an l-lysine auxotrophic, naturally sucrose-negative E. coli strain with a C. glutamicum strain able to produce l-lysine that secretes fructose when grown with sucrose due to deletion of the fructose importer gene ptsF. Mutualistic synthetic consortia with an l-lysine auxotrophic, α-amylase secreting E. coli strain and naturally amylase-negative C. glutamicum strains was implemented for production of valuable fine chemicals from starch.
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Affiliation(s)
- Elvira Sgobba
- Chair of Genetics of Prokaryotes, Faculty of Biology & CeBiTec, Bielefeld University, Bielefeld, Germany
| | - Anna K Stumpf
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität (WWU) Münster, Germany
| | - Marina Vortmann
- Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität (WWU) Münster, Germany
| | - Nina Jagmann
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität (WWU) Münster, Germany
| | | | | | - Bruno Moerschbacher
- Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität (WWU) Münster, Germany
| | - Bodo Philipp
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität (WWU) Münster, Germany
| | - Volker F Wendisch
- Chair of Genetics of Prokaryotes, Faculty of Biology & CeBiTec, Bielefeld University, Bielefeld, Germany.
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Jiang L, Dai J, Sun Y, Xiu Z. The effects of ionic liquid 1-ethyl-3-methylimidazolium trifluoromethanesulfonate on the production of 1,3-propanediol from crude glycerol by microbial consortium. Bioprocess Biosyst Eng 2018; 41:1079-1088. [DOI: 10.1007/s00449-018-1937-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 04/08/2018] [Indexed: 11/28/2022]
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Mourad EF, Sarhan MS, Daanaa HSA, Abdou M, Morsi AT, Abdelfadeel MR, Elsawey H, Nemr R, El-Tahan M, Hamza MA, Abbas M, Youssef HH, Abdelhadi AA, Amer WM, Fayez M, Ruppel S, Hegazi NA. Plant Materials are Sustainable Substrates Supporting New Technologies of Plant-Only-Based Culture Media for in vitro Culturing of the Plant Microbiota. Microbes Environ 2018; 33:40-49. [PMID: 29479006 PMCID: PMC5877342 DOI: 10.1264/jsme2.me17135] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
In order to improve the culturability and biomass production of rhizobacteria, we previously introduced plant-only-based culture media. We herein attempted to widen the scope of plant materials suitable for the preparation of plant-only-based culture media. We chemically analyzed the refuse of turfgrass, cactus, and clover. They were sufficiently rich to support good in vitro growth by rhizobacteria isolates representing Proteobacteria and Firmicutes. They were also adequate and efficient to produce a cell biomass in liquid batch cultures. These culture media were as sufficient as artificial culture media for the cultivation and recovery of the in situ rhizobacteria of barley (Hordeum murinum L.). Based on culture-dependent (CFU plate counting) and culture-independent analyses (qPCR), mowed turfgrass, in particular, supported the highest culturable population of barley endophytes, representing >16% of the total bacterial number quantified with qPCR. This accurately reflected the endophytic community composition, in terms of diversity indices (S', H', and D') based on PCR-DGGE, and clustered the plant culture media together with the qPCR root populations away from the artificial culture media. Despite the promiscuous nature of the plant materials tested to culture the plant microbiome, our results indicated that plant materials of a homologous nature to the tested host plant, at least at the family level, and/or of the same environment were more likely to be selected. Plant-only-based culture media require further refinements in order to provide selectivity for the in vitro growth of members of the plant microbiome, particularly difficult-to-culture bacteria. This will provide insights into their hidden roles in the environment and support future culturomic studies.
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Affiliation(s)
| | - Mohamed S Sarhan
- Department of Microbiology, Faculty of Agriculture, Cairo University
| | | | - Mennatullah Abdou
- Department of Microbiology, Faculty of Agriculture, Cairo University
| | - Ahmed T Morsi
- Department of Microbiology, Faculty of Agriculture, Cairo University
| | | | - Hend Elsawey
- Department of Microbiology, Faculty of Agriculture, Cairo University
| | - Rahma Nemr
- Department of Microbiology, Faculty of Agriculture, Cairo University
| | - Mahmoud El-Tahan
- Regional Center for Food & Feed (RCFF), Agricultural Research Center
| | - Mervat A Hamza
- Department of Microbiology, Faculty of Agriculture, Cairo University
| | - Mohamed Abbas
- Department of Microbiology, Faculty of Agriculture & Natural Resources, Aswan University
| | - Hanan H Youssef
- Department of Microbiology, Faculty of Agriculture, Cairo University
| | | | - Wafaa M Amer
- Department of Botany and Microbiology, Faculty of Science, Cairo University
| | - Mohamed Fayez
- Department of Microbiology, Faculty of Agriculture, Cairo University
| | - Silke Ruppel
- Leibniz Institute of Vegetable and Ornamental Crops (IGZ)
| | - Nabil A Hegazi
- Department of Microbiology, Faculty of Agriculture, Cairo University
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Wu W, Liu X, Zhang X, Zhu M, Tan W. Bioleaching of copper from waste printed circuit boards by bacteria-free cultural supernatant of iron–sulfur-oxidizing bacteria. BIORESOUR BIOPROCESS 2018. [DOI: 10.1186/s40643-018-0196-6] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
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Bagheri B, Bauer FF, Setati ME. The Impact of Saccharomyces cerevisiae on a Wine Yeast Consortium in Natural and Inoculated Fermentations. Front Microbiol 2017; 8:1988. [PMID: 29085347 PMCID: PMC5650610 DOI: 10.3389/fmicb.2017.01988] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 09/27/2017] [Indexed: 11/25/2022] Open
Abstract
Natural, also referred to as spontaneous wine fermentations, are carried out by the native microbiota of the grape juice, without inoculation of selected, industrially produced yeast or bacterial strains. Such fermentations are commonly initiated by non-Saccharomyces yeast species that numerically dominate the must. Community composition and numerical dominance of species vary significantly between individual musts, but Saccharomyces cerevisiae will in most cases dominate the late stages of the fermentation and complete the process. Nevertheless, non-Saccharomyces species contribute significantly, positively or negatively, to the character and quality of the final product. The contribution is species and strain dependent and will depend on each species or strain's absolute and relative contribution to total metabolically active biomass, and will therefore, be a function of its relative fitness within the microbial ecosystem. However, the population dynamics of multispecies fermentations are not well understood. Consequently, the oenological potential of the microbiome in any given grape must, can currently not be evaluated or predicted. To better characterize the rules that govern the complex wine microbial ecosystem, a model yeast consortium comprising eight species commonly encountered in South African grape musts and an ARISA based method to monitor their dynamics were developed and validated. The dynamics of these species were evaluated in synthetic must in the presence or absence of S. cerevisiae using direct viable counts and ARISA. The data show that S. cerevisiae specifically suppresses certain species while appearing to favor the persistence of other species. Growth dynamics in Chenin blanc grape must fermentation was monitored only through viable counts. The interactions observed in the synthetic must, were upheld in the natural must fermentations, suggesting the broad applicability of the observed ecosystem dynamics. Importantly, the presence of indigenous yeast populations did not appear to affect the broad interaction patterns between the consortium species. The data show that the wine ecosystem is characterized by both mutually supportive and inhibitory species. The current study presents a first step in the development of a model to predict the oenological potential of any given wine mycobiome.
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Affiliation(s)
| | | | - Mathabatha E. Setati
- Department of Viticulture and Oenology, Institute for Wine Biotechnology, Stellenbosch University, Stellenbosch, South Africa
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Cortes-Tolalpa L, Salles JF, van Elsas JD. Bacterial Synergism in Lignocellulose Biomass Degradation - Complementary Roles of Degraders As Influenced by Complexity of the Carbon Source. Front Microbiol 2017; 8:1628. [PMID: 29067002 PMCID: PMC5641323 DOI: 10.3389/fmicb.2017.01628] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 08/10/2017] [Indexed: 01/23/2023] Open
Abstract
Lignocellulosic biomass (LCB) is an attractive source of carbon for the production of sugars and other chemicals. Due to its inherent complexity and heterogeneity, efficient biodegradation requires the actions of different types of hydrolytic enzymes. In nature, complex microbial communities that work efficiently and often synergistically accomplish degradation. Studying such synergisms in LCB degradation is fundamental for the establishment of an optimal biological degradation process. Here, we examine the wheat straw degradation potential of synthetic microbial consortia composed of bacteria and fungi. Growth of, and enzyme secretion by, monocultures of degrader strains were studied in aerobic cultures using wheat straw as the sole carbon and energy source. To investigate synergism, co-cultures were constructed from selected strains and their performance was tested in comparison with the respective monocultures. In monoculture, each organism – with a typical enzymatic profile – was found to mainly consume the cellulose part of the substrate. One strain, Flavobacterium ginsengisoli so9, displayed an extremely high degradation capacity, as measured by its secreted enzymes. Among 13 different co-cultures, five presented synergisms. These included four bacterial bicultures and one bacterial–fungal triculture. The highest level of synergism was found in a Citrobacter freundii/Sphingobacterium multivorum biculture, which revealed an 18.2-fold increase of the produced biomass. As compared to both monocultures, this bacterial pair showed significantly increased enzymatic activities, in particular of cellobiohydrolases, mannosidases, and xylosidases. Moreover, the synergism was unique to growth on wheat straw, as it was completely absent in glucose-grown bicultures. Spent supernatants of either of the two partners were found to stimulate the growth on wheat straw of the counterpart organism, in a directional manner. Thus, the basis of the LCB-specific synergism might lie in the specific release of compounds or agents by S. multivorum w15 that promote the activity of C. freundii so4 and vice versa.
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Affiliation(s)
- Larisa Cortes-Tolalpa
- Department of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
| | - Joana F Salles
- Department of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
| | - Jan Dirk van Elsas
- Department of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
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